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loss and loss_aggregator. There is a new vignette that showcases this new feature.adjust_labels in plot.euler() has been deprecated and removed to fix sanitizer warnings.inst/CITATIONPI to M_PI to support STRICT_R_HEADERS in C++ code (#82, thanks @eddelbuettel)euler() with adjust_labels = TRUE) no longer repels text labels away from the edges of the shapes in the diagram.stringsAsFactors = TRUE inside all relevant functions in euler() to avoid errors in upcoming R version.venn() exceeds 5 (##65)euler() and venn() (##64, @privefl)data.frame inputs to euler() when categorical variables are character vectors and not factors.plot.euler(), percentages can be added to the plot in addition to or instead of counts by providing a list to the quantities argument with an item type that can take any combination of counts and percent. This change also comes with a redesign of the grid graphics implementation for labels.eulerr_options() gains a new argument padding which controls the amount of padding between labels and quantities. (##48)plot.euler() now uses code from the ggrepel package to prevent labels from overlapping or escaping the plot area if adjust_labels is set to TRUE.cex for quantity labels has changed from 1.0 to 0.9.data slot in the object created by calling to plot.euler() (##57)venn() is a new function that produces Venn diagrams for up to 5 sets. The interface is almost identical to euler() except that a single integer can also be provided. A new vignette, Venn diagrams with eulerr, exemplifies its use.plot.euler() when a list of Euler diagrams is given has been improved. Setting fontsize or cex now results in appropriately sized strips as one would expect.eulergram() objects from plot.euler() now have a proper grob name for the canvas grob, so that extracting information from them is easier.euler() now correctly says “ellipses” and not “coefficients”.data.frame or matrix inputs now work properly when values are numerical. (##42)error_plot() is a new function that offers diagnostic plots of fits from euler(), letting the user visualize the error in the resulting Euler diagram.euler() once again uses the residual sums of squares, rather than the stress metric, as optimization objective, which means that output is always scaled appropriately to input (##28).plot.euler() now uses the polylabelr package to position labels for the overlaps of the ellipses, which has improved performance in plotting complicated diagrams considerably and reduced the amount of code in this package greatly.euler.data.frame() method (and by proxy the euler.matrix() method) can now take matrices with factors in addition to the previously supported logical and integer (binary) input. The function will dummy code the variables for the user.plot.euler() have been made defunct.plants, to exemplify the list method for euler().fruits, to exemplify the data.frame method for euler().euler.data.frame() gains an argument sep, which is a character vector used to separate dummy-coded factors if there are factors or characters in the input.organisms, to exemplify the matrix method for euler().pain, to exemplify the table method for euler().euler.table() gains an argument, factor_names, for specifying whether the factor names should be included when generating dummy-coded variables in case the input is a data.frame with character or factor vectors or if the input is a table with more than two columns or rows.euler.list() now passes its ellipsis argument along properly. (##33, thanks, @banfai)plot.euler() now returns a gTree object. All of the plotting mechanisms are now also found in this function and plot.eulergram() and print.eulergram() basically just call grid::grid.draw() on the result of plot.euler(). This change means that functions such as gridExtra::grid.arrange() now work as one would intuit on the objects produced by plot.euler().NA in the resulting data.frame of ellipses.GenSA::GenSA() from RcppDE::DEoptim().plot.euler().euler.data.frame() now works as expected for tibbles (from the tibble package) when argument by is used.plot.euler() has been rewritten completely from scratch, now using a custom grid-based implementation rather than lattice. As a result, all panel.*() functions and label() have been deprecated as well as arguments fill_alpha, auto.key, fontface, par.settings, default.prepanel, default.scales, and panel. The method for plotting diagrams has also changed—rather than overlaying shapes on top of each other, the diagram is now split into separate polygons using the polyclip package. Instead of relying on semi-transparent fills, the colors of the fills are now blended in the CIELab color space (##16).eulerr_options() have been provided in order to set default graphical parameters for the diagrams.counts and outer_strips to plot.euler() are now defunct.euler() now always returns ellipse-based parameters with columns h, k, a, b, and phi, regardless of which shape is used. This item was previously named “coefficients”, but it now called “ellipses” instead and a custom coef.euler() method has been added to make cure that coef() still works.quantities and labels arguments of plot.euler() now works correctly (##20).GenSA::GenSA() to RcppDE::DEoptim().stats::nlm() again.label is now a proper generic with an appropriate method (label.euler()).counts argument in one of the vignettes.auto.key = TRUE and labels were not in alphabetic order. (##15)shape = "ellipse" in euler(). This functionality accompanies an overhaul of the innards of the function.stats::optim(..., method = "L-BFGS-B") to stats::nlminb().GenSA::GenSA() when the fit from nlminb() isn’t good enough, by default for 3 sets and ellipses, but this behavior can be controlled via a new argument control.diagError and regionError metrics have been changed from diag_error and region_error to reflect the original names.label() function has been added to extract locations for the overlaps for third party plotting (##10).counts argument to plot.euler() and panel.euler.labels() have been deprecated in favor of the more appropriate quantities.fill_opacity in plot.euler() that was deprecated in v2.0.0 has been made defunct.eulerr() has been replaced with euler() (see update 1.1.0) and made defunct.euler:
euler.list() produces diagrams from a list of sample spaces.euler.table() produces diagrams from a table object, as long as there are no dimensions with values greater than 2.plot.euler() has been rewritten (again) from the ground up to better match other high-level functions from lattice. This change is intended to be as smooth as possible and should not make much of a difference to most users.polygon_args, mar, and text_args to plot.euler() have been made defunct.plot.euler() handles conflicting arguments better.eulerr now use registration.euler() now allows single sets (##9).plot.euler() now use a bold font face by default in order to distinguish them from the typeface used for counts.key in plot.euler() has been deprecated and replaced with auto.key. Notice that using key does not throw a warning since the argument is used in lattice::xyplot() (which plot.euler() relies on).fill_opacity is softly deprecated and has been replaced with fill_alpha for consistency with other lattice functions.border argument in plot.euler() works again (##7).eulerr() and its related methods been deprecated and are being replaced by euler(), which takes slightly different input. Notably, the default is now to provide input in the form of disjoint class combinations, rather than unions. This is partly to make the function a drop-in replacement for venneuler::venneuler.plot.euler() has been completely revamped, now interfacing xyplot() from lattice. As a result, arguments polygon_args, mar, and text_args have been deprecated.counts argument to plot.eulerr, which intersections and complements with counts from the original set specification (##6).key argument to plot.eulerr that prints a legend next to the diagram.atan2() from RcppArmadillo.cost and now forces the function to use sums of squares, which is more or less equivalent to the cost function from venneuler.plot.euler() now chooses colors adapted to color vision deficiency (deuteranopia). With increasingly large numbers of sets, this adaptation is relaxed to make sure that colors are kept visually distinct.euler() now uses nlm() instead of optim(method = "Nelder-Mead") for its final optimization.print.eulerr.cost argument (currently eulerAPE or venneuler).by argument to eulerr. The result is a list of Euler diagrams that can be plotted in a grid arrangement via a new plot method.mar argument to plot.eulerr with a default that produces symmetric margins.stress statistic from venneuler.print.eulerr method.These binaries (installable software) and packages are in development.
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